Locus 1851

Sequence ID 2L_DroMel_CAF1
Location 5,088,809 – 5,089,017
Length 208
Max. P 0.998078
window2981 window2982 window2983 window2984

overview

Window 1

Location 5,088,809 – 5,088,912
Length 103
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.52
Mean single sequence MFE -31.04
Consensus MFE -26.52
Energy contribution -26.33
Covariance contribution -0.19
Combinations/Pair 1.05
Mean z-score -2.04
Structure conservation index 0.85
SVM decision value 1.21
SVM RNA-class probability 0.930536
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5088809 103 - 22407834
GAUGGGUCUAGAAAUUAGCCAAGUUGACAACGCUGAGCAACGAAACGCGUCAGCAACAAUGGCUGCAUUAACAACAAAGGUCCAAUGC---------------AGCAGCCAGCACAGC--
....(((..(....)..)))..((((.(...(((((((........)).))))).......((((((((.((.......))..)))))---------------))).).)))).....-- ( -28.40)
>DroSec_CAF1 18194 105 - 1
GAUGGGUCUAGAAAUUAGCCAAGUUGACAACGCUGAGCAACGAAACGCGUCAGCAACAAUGGCUGCAUUAACAACAAAGGUCCAAUGC---------------UGCAGCCAGCACAGCAC
....(((..(....)..)))..((((.....(((((((........)).))))).....((((((((......((....)).......---------------))))))))...)))).. ( -29.62)
>DroSim_CAF1 20808 105 - 1
GAUGGGUCUAGAAAUUAGCCAAGUUGACAACGCUGAGCAACGAAACGCGUCAGCAACAAUGGCUGCAUUAACAACAAAGGUCCAAUGC---------------UGCAGCCAGCACAGCAC
....(((..(....)..)))..((((.....(((((((........)).))))).....((((((((......((....)).......---------------))))))))...)))).. ( -29.62)
>DroYak_CAF1 19774 118 - 1
GAUUGGUCUGGAAAUUGGCCAGGUUGACAACGCUGAGCAGCGAAACGCGUCAGCAACAAUGGCUGCAUAAACAACAAAGCUUCCAUGCAACAGCAGCAGUAGCAGCAGCCAGCACAGC--
..((((((........))))))((((.....(((((...(((...))).))))).....(((((((...................(((....)))((....)).)))))))...))))-- ( -36.50)
>consensus
GAUGGGUCUAGAAAUUAGCCAAGUUGACAACGCUGAGCAACGAAACGCGUCAGCAACAAUGGCUGCAUUAACAACAAAGGUCCAAUGC_______________AGCAGCCAGCACAGC__
....(((..(....)..)))..((((.....(((((((........)).))))).....(((((((......................................)))))))...)))).. (-26.52 = -26.33 +  -0.19)

alignment

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secondary structure

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Window 2

Location 5,088,832 – 5,088,952
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.47
Mean single sequence MFE -38.10
Consensus MFE -35.56
Energy contribution -35.75
Covariance contribution 0.19
Combinations/Pair 1.07
Mean z-score -1.72
Structure conservation index 0.93
SVM decision value 0.89
SVM RNA-class probability 0.875636
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5088832 120 + 22407834
CCUUUGUUGUUAAUGCAGCCAUUGUUGCUGACGCGUUUCGUUGCUCAGCGUUGUCAACUUGGCUAAUUUCUAGACCCAUCUGGUUAUUGCCAACCGGCGGAAAUGGCAAGAACAAUGCUC
.....((((((..(((((((((((.((((((.(((......)))))))))....)))..))))).((((((.((((.....))))...(((....))))))))).)))..)))))).... ( -37.60)
>DroSec_CAF1 18219 120 + 1
CCUUUGUUGUUAAUGCAGCCAUUGUUGCUGACGCGUUUCGUUGCUCAGCGUUGUCAACUUGGCUAAUUUCUAGACCCAUCUGGUUACUGCCAAGCGGCGGAAAUGGCAAGAACAAUGCUC
.....((((((......((((((...(((((.(((......)))))))).(((((..((((((......(((((....))))).....)))))).))))).))))))...)))))).... ( -37.90)
>DroSim_CAF1 20833 120 + 1
CCUUUGUUGUUAAUGCAGCCAUUGUUGCUGACGCGUUUCGUUGCUCAGCGUUGUCAACUUGGCUAAUUUCUAGACCCAUCUGGUUAUUACCAAGCGGCGGAAAUGGCAAGAACAAUGCUC
.....((((((......((((((...(((((.(((......)))))))).(((((..(((((.((((..(((((....)))))..))))))))).))))).))))))...)))))).... ( -37.60)
>DroYak_CAF1 19812 120 + 1
GCUUUGUUGUUUAUGCAGCCAUUGUUGCUGACGCGUUUCGCUGCUCAGCGUUGUCAACCUGGCCAAUUUCCAGACCAAUCUGGUUAAUGCCAAGGGGCGGAUGUGGCAAGAACAAUACCC
....((((((((.(((.(((((((.((((((.(((......)))))))))....)))..))))((...(((.((((.....))))...(((....))))))..))))).))))))))... ( -39.30)
>consensus
CCUUUGUUGUUAAUGCAGCCAUUGUUGCUGACGCGUUUCGUUGCUCAGCGUUGUCAACUUGGCUAAUUUCUAGACCCAUCUGGUUAUUGCCAAGCGGCGGAAAUGGCAAGAACAAUGCUC
....(((((((..(((((((((((.((((((.(((......)))))))))....)))..))))).((((((.((((.....))))...(((....))))))))).)))..)))))))... (-35.56 = -35.75 +   0.19)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,088,872 – 5,088,992
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.28
Mean single sequence MFE -37.98
Consensus MFE -32.61
Energy contribution -33.55
Covariance contribution 0.94
Combinations/Pair 1.08
Mean z-score -2.76
Structure conservation index 0.86
SVM decision value 2.08
SVM RNA-class probability 0.987437
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5088872 120 + 22407834
UUGCUCAGCGUUGUCAACUUGGCUAAUUUCUAGACCCAUCUGGUUAUUGCCAACCGGCGGAAAUGGCAAGAACAAUGCUCAUUUUGUGGGCAACCACAAGUCAGUUUAAAGUGCAAAACU
((((.(((((((((...((((.(((.(((((.((((.....))))...(((....))))))))))))))).))))))))...(((((((....)))))))..........).)))).... ( -39.20)
>DroSec_CAF1 18259 120 + 1
UUGCUCAGCGUUGUCAACUUGGCUAAUUUCUAGACCCAUCUGGUUACUGCCAAGCGGCGGAAAUGGCAAGAACAAUGCUCACUUUGUGGGCAACCACAAGUUAGUUUGAAUUGCAAAACU
((((..((((((((...((((.(((....(((((....)))))...(((((....)))))...))))))).))))))))...(((((((....)))))))............)))).... ( -38.30)
>DroSim_CAF1 20873 120 + 1
UUGCUCAGCGUUGUCAACUUGGCUAAUUUCUAGACCCAUCUGGUUAUUACCAAGCGGCGGAAAUGGCAAGAACAAUGCUCAAUUUGUGGGCAACCACAAGUUAGUUUGAAUUGCAAAACU
((((..(((((((((..(((((.((((..(((((....)))))..)))))))))..((.......))..).)))))))).(((((((((....)))))))))..........)))).... ( -39.50)
>DroYak_CAF1 19852 120 + 1
CUGCUCAGCGUUGUCAACCUGGCCAAUUUCCAGACCAAUCUGGUUAAUGCCAAGGGGCGGAUGUGGCAAGAACAAUACCCAUUUUGUGGGCAACCACAAGUCAGUUUCAUUUUCAUGACU
.((((..((((((((..((((((......(((((....))))).....))).)))))).)))))))))...............((((((....))))))((((............)))). ( -34.90)
>consensus
UUGCUCAGCGUUGUCAACUUGGCUAAUUUCUAGACCCAUCUGGUUAUUGCCAAGCGGCGGAAAUGGCAAGAACAAUGCUCAUUUUGUGGGCAACCACAAGUCAGUUUGAAUUGCAAAACU
((((...(((((((...((((.(((.(((((.((((.....))))...(((....))))))))))))))).)))))))....(((((((....)))))))............)))).... (-32.61 = -33.55 +   0.94)

alignment

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secondary structure

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dotplot

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Window 4

Location 5,088,912 – 5,089,017
Length 105
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 79.37
Mean single sequence MFE -32.08
Consensus MFE -20.90
Energy contribution -22.39
Covariance contribution 1.50
Combinations/Pair 1.12
Mean z-score -3.01
Structure conservation index 0.65
SVM decision value 3.00
SVM RNA-class probability 0.998078
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5088912 105 + 22407834
UGGUUAUUGCCAACCGGCGGAAAUGGCAAGAACAAUGCUCAUUUUGUGGGCAACCACAAGUCAGUUUAAAGUGCAAAACUAAUUAAGCCGUGGUACUUAAACAG---U------------
((((....))))...(((.(((((((((.......))).))))))((((....))))..))).((((((.((((...((..........)).))))))))))..---.------------ ( -29.60)
>DroSec_CAF1 18299 103 + 1
UGGUUACUGCCAAGCGGCGGAAAUGGCAAGAACAAUGCUCACUUUGUGGGCAACCACAAGUUAGUUUGAAUUGCAAAACUAAUCAAG-----GUAAUAAAGCUGCUGU------------
((((....))))((((((.......((((...(((.(((.((((.((((....)))))))).))))))..))))...(((......)-----))......))))))..------------ ( -32.80)
>DroSim_CAF1 20913 103 + 1
UGGUUAUUACCAAGCGGCGGAAAUGGCAAGAACAAUGCUCAAUUUGUGGGCAACCACAAGUUAGUUUGAAUUGCAAAACUAAUCAAG-----GUAAUAAAGCUGUUGU------------
((((....))))((((((.......((((...(((.(((.(((((((((....)))))))))))))))..))))...(((......)-----))......))))))..------------ ( -31.70)
>DroYak_CAF1 19892 115 + 1
UGGUUAAUGCCAAGGGGCGGAUGUGGCAAGAACAAUACCCAUUUUGUGGGCAACCACAAGUCAGUUUCAUUUUCAUGACUAAUCAAU-----GUUAUAAAGCUGCUGUAUCUAAGCUUCU
((((....))))(((((((((((..(((.(((..........(((((((....)))))))...........)))(((((........-----))))).....)))..)))))..)))))) ( -34.20)
>consensus
UGGUUAUUGCCAAGCGGCGGAAAUGGCAAGAACAAUGCUCAUUUUGUGGGCAACCACAAGUCAGUUUGAAUUGCAAAACUAAUCAAG_____GUAAUAAAGCUGCUGU____________
((((....))))((((((.......((................((((((....))))))((((((((........)))))))).........))......)))))).............. (-20.90 = -22.39 +   1.50)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:59 2006